mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | CP000731 | 81 | N→G | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 25,669 | (A)7→6 | coding (322/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 26,506 | C→G | R281G (CGC→GGC) | walK → | Sensor protein kinase WalK |
| RA | USA300TCH1516_ALE | 603,961 | G→A | M464I (ATG→ATA) | araB → | Ribulokinase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,744,446 | G→A | P76S (CCT→TCT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,899,742 | A→G | N421N (AAT→AAC) | USA300HOU_RS09405 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,030,815 | G→T | A90S (GCA→TCA) | USA300HOU_RS10250 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,722,719 | C→T | G13D (GGT→GAT) | yciC_3 ← | Putative metal chaperone YciC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | USA300TCH1516_ALE | 58657 | 58991 | 335 | 9 [7] | [6] 8 | USA300TCH1516_00049/USA300HOU_RS00245 | hypothetical protein/hypothetical protein |
| * | * | ÷ | USA300TCH1516_ALE | 346033 | 346152 | 120 | 8 [7] | [7] 8 | [USA300HOU_RS01550] | [USA300HOU_RS01550] |
| * | * | ÷ | USA300TCH1516_ALE | 1562007 | 1562247 | 241 | 9 [7] | [6] 8 | [hlgC_1] | [hlgC_1] |
| * | * | ÷ | USA300TCH1516_ALE | 2089630 | 2089722 | 93 | 9 [7] | [7] 8 | sak/lytN_3 | Staphylokinase/putative cell wall hydrolase LytN |
| * | * | ÷ | USA300TCH1516_ALE | 2348638 | 2348840 | 203 | 8 [6] | [6] 8 | [USA300HOU_RS11980]–[clpB_3] | [USA300HOU_RS11980],[clpB_3] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 42 (0.540) | 51 (0.930) +40 bp |
42/188 | 0.2 | 63.4% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||